By Ellen Nakashima

On the day he disappeared, Jacinto da Costa Canisio Pereira, a local resistance leader, stood in a priest's bedroom and prayed, his brother recalled.
"I wanted to stay, to die with my brother," said Graciano Pires dos Santos. His knuckles, head and legs bear scars from machete, hammer and bullet wounds inflicted by Indonesian soldiers and the Timorese militiamen they sponsored, who stormed Sao Joao de Brito Church in April 1999. But as gunshots rang out and tear gas stung their eyes, Pereira urged him to leave, he recounted.
Pereira was among about 1,500 people killed in East Timor in a series of massacres in 1999 at the time of its referendum for independence from Indonesia.

Time has not dimmed the survivors' memories or fervor. In interviews last month in villages across this small island nation, the victims' families said they wanted to know the truth. Who murdered their relatives, who gave the orders, where are the bodies? But the truth, they said, is not sufficient. The survivors, who in some cases live near the people who burned their houses or carted away the bodies, hunger for justice: They want the killers charged and tried in an impartial court of law.

The families' insistence on prosecutions puts them at direct odds with their government, whose leaders, veterans of the 24-year struggle for independence from Indonesia, now want friendship with the former occupier. The two countries have created a Commission on Truth and Friendship, modeled after South Africa's post-apartheid panel. The commission's aim is to establish the "conclusive truth" about the crimes up to and after the August 1999 vote; its work will not lead to prosecutions.

The 10-member panel, formed in August with a one-year term, has the power to recommend amnesty for people who fully explain their crimes, apologize and show remorse. It contains no provision for criminal proceedings or compensation. The lack of prosecution, critics warn, is a recipe for impunity.
"What's more important for us?" said Jose Ramos-Horta, East Timor's foreign minister, who proposed the commission to the Jakarta government. "That democracy slowly is consolidated in Indonesia? Or the blind pursuit of justice at the expense of stability in Indonesia?"

Ramos-Horta, a 1996 Nobel Peace laureate who spent 24 years in exile, and President Xanana Gusmao, a charismatic former freedom fighter who spent more than six years in a Jakarta prison, oppose survivors' calls for an international war crimes tribunal. The Timor government also has rejected a recommendation by a U.N. advisory panel that the Indonesian government redo its widely criticized East Timor war crimes trials. The trials concluded last year with only one of 18 defendants convicted. New trials, Ramos-Horta asserted, would prompt a backlash within Indonesia's powerful military and destabilize East Timor's fledgling democracy.
"Truth is already a major aspect of justice," he said, leaning back in a swivel chair in his office in the government palace overlooking the Indian Ocean.

"They're playing word games," said an indignant Rafael dos Santos, the Liquica parish priest in 1999 and now a Catholic school principal in Dili, the capital. "A crime is a crime. Justice is justice."

The day before the April 6, 1999, massacre, waves of anti-independence militiamen advanced over the hills into Liquica, a town of about 55,000. Hundreds of men, women and children flocked to the church compound on a hillside sloping to the sea, believing they would be safe there. The Indonesian-trained militiamen were burning homes and kidnapping resistance leaders, said the priest and other survivors, whose recollections, along with an indictment from a U.N.-funded prosecution team, form the basis for the following account:

Shortly before 1 p.m. on April 6, a militia leader approached the compound and asked that Pereira, who was a village chief, and other resistance members surrender. They refused.
At 1 p.m., a shot rang out. Hundreds of militiamen, soldiers and police officers surrounded the compound. Police fired tear gas. Bullets flew.

"People started running every which way," said Helio Domingos da Costa, Pereira's oldest son, now 22. "The militia started to attack, swinging machetes. . . . I was running wildly when suddenly a militiaman came up." He made a swooping motion with his right arm. "I moved. He missed. Then he yelled, 'Now go inside and die with your father!' "

Pereira and several other resistance members were hiding in the priest's bedroom and adjoining bathroom. Several teenagers hid in the crawl space between the ceiling and the zinc roof. Troops climbed on the roof and fired down.
Dos Santos, the priest, was escorted to the district military command by a nephew, who was an Indonesian soldier. As the priest was leaving, Pereira's brother recalled, "I saw many people inside the house try to grab Father Rafael's robes, touching them and shouting, 'We are dying! We are dying!' "

Pereira's wife could hear the gunfire from a brother-in-law's house, where she had fled with her three youngest children. The militiamen burned her house. That afternoon, an Indonesian soldier's wife told her that the men who had hidden in the priest's home had been killed. "I felt like I wanted to cry," she said, "but no tears came."

About 5 p.m., the priest returned to the church. He found no bodies, but blood was on the bathroom and bedroom floor, along with part of a brain. A few days later, the military had mopped up the blood, repaired the roof and patched the bullet-pocked plaster in an apparent attempt to cover up the massacre, said the priest, who showed a reporter a scarred memento: a white robe bearing singed holes from bullets that penetrated his closet.

Authorities initially said five people were killed. Liquica police later told the priest that 113 had been killed. The U.N. indictment stated that more than 50 civilians had been murdered.
So far, only one person has been tried and convicted in connection with the massacre. Pereira's murder case is still open; no one has been indicted, according to U.N. records.

Three times in the last six years, Anita dos Santos, who is Pereira's widow, and her neighbors have searched for their relatives' bodies. Using shovels and buckets, they have dug in Liquica, in a neighboring town and in a village by the sea. "People would come to say, 'This is the site. Dig here,' " she said. "So we tried. Many times, we tried. We found nothing."
She nodded toward a family graveyard 120 yards away, nestled amid coconut and tamarind trees. She dreams, she said, of being able to bury her husband's remains there, in a row of stone tombs.

Lower-level militia members who burned and looted homes now live in Liquica, said Eliza da Silva dos Santos, the widow of a resistance member who was "disappeared" with Pereira. "Sometimes I see them on the street, driving a car, working in a government office," she said bitterly. "When I see them, it pains me." She must repress an urge, she said, to attack them.

The survivors' frustration is deepened by a sense of betrayal by their own government and the United Nations. For years, Eliza dos Santos and Anita dos Santos helped the underground resistance, passing supplies to rebels. They, like their husbands, revered Gusmao, the prisoner turned president. Now, they charge, he and Ramos-Horta, the foreign minister, have forgotten "the little people." The women also criticize the United Nations for closing its special prosecution unit in May, leaving pending more than 600 cases linked to the 1999 crimes.

Over 4 1/2 years, the U.N.-funded unit convicted only 84 people, all low- to mid-level Timorese militia members. The higher-ranking personnel, including Indonesian military and police officers, are beyond reach in Indonesia, which has no extradition treaty with East Timor.
Topping the impunity list is Gen. Wiranto, the retired Indonesian military commander, indicted by a Dili prosecutor. For political reasons, the warrant was never forwarded to Interpol, the international police agency.
Two months ago, Ramos-Horta said, he warned Wiranto that the truth commission was "their last chance to clean Indonesia's image." Wiranto, he said, promised cooperation.

The survivors of the struggle for independence also criticize the impunity of those among the Indonesian security forces who committed abuses. An estimated 150,000 to 175,000 Timorese -- up to one-fourth of the population -- were killed during Indonesia's occupation of East Timor.
Aniceto Guterres, a truth commission member and human rights lawyer who was an early proponent of an international tribunal, has deep misgivings about the panel's lack of a prosecution option. But "if I had to choose between truth and justice," he said, "I would opt for truth."

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